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Yorodumi- PDB-4qy1: Structure of H10 from human-infecting H10N8 in complex with avian... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qy1 | |||||||||
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Title | Structure of H10 from human-infecting H10N8 in complex with avian receptor | |||||||||
Components | (hemagglutinin) x 2 | |||||||||
Keywords | VIRAL PROTEIN / receptor binding / memebrane fusion | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å | |||||||||
Authors | Wang, M. / Zhang, W. / Qi, J. / Wang, F. / Zhou, J. / Bi, Y. / Wu, Y. / Sun, H. / Liu, J. / Huang, C. ...Wang, M. / Zhang, W. / Qi, J. / Wang, F. / Zhou, J. / Bi, Y. / Wu, Y. / Sun, H. / Liu, J. / Huang, C. / Li, X. / Yan, J. / Shu, Y. / Shi, Y. / Gao, G.F. | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structural basis for preferential avian receptor binding by the human-infecting H10N8 avian influenza virus Authors: Wang, M. / Zhang, W. / Qi, J. / Wang, F. / Zhou, J. / Bi, Y. / Wu, Y. / Sun, H. / Liu, J. / Huang, C. / Li, X. / Yan, J. / Shu, Y. / Shi, Y. / Gao, G.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qy1.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4qy1.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 4qy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qy1_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4qy1_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4qy1_validation.xml.gz | 215.6 KB | Display | |
Data in CIF | 4qy1_validation.cif.gz | 294.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/4qy1 ftp://data.pdbj.org/pub/pdb/validation_reports/qy/4qy1 | HTTPS FTP |
-Related structure data
Related structure data | 4qy0C 4qy2C 4bsgS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX
#1: Protein | Mass: 34830.293 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Jiangxi-Donghu/346/2013(H10N8) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A059T4A1*PLUS #2: Protein | Mass: 19987.896 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Jiangxi-Donghu/346/2013(H10N8) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A059T4A1*PLUS |
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-Sugars , 3 types, 30 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#4: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine #5: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 1513 molecules
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 15%(w/v) PEG 2000 MME, 0.1M potassium chloride, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2014 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.594→50 Å / Num. all: 262929 / Num. obs: 262929 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.4 Å2 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BSG Resolution: 2.594→37.073 Å / FOM work R set: 0.7935 / SU ML: 0.35 / σ(F): 1.96 / Phase error: 27.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.54 Å2 / Biso mean: 38.29 Å2 / Biso min: 3.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.594→37.073 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Origin x: -21.8614 Å / Origin y: 62.2385 Å / Origin z: -17.2672 Å
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Refinement TLS group | Selection details: ALL |